R/summarizeAll.R

In strataG: Summaries and Population Structure Analyses of Genetic Data

#' @title Summarize Genotypes and Sequences
#' @description Conducts a suite of data summaries. Summarizes missing data and 
#'   homozygosity by individual and locus, and looks for duplicate genotypes 
#'   (see \code{\link{dupGenotypes}}). For sequence data, identifies low 
#'   frequency substitutions (see \code{\link{lowFreqSubs}}), and computes 
#'   sequence likelihoods (see \code{\link{sequenceLikelihoods}}).
#' 
#' @param g a \linkS4class{gtypes} object.
#' @param write.files logical determining whether to write .csv files of 
#'   summaries
#' @param label optional label for output folder and prefix for files.
#' @param ... optional arguments to pass on to summary functions.
#' 
#' @return If \code{write.files = TRUE}, files are written for by-sample and 
#'   by-locus summaries, and duplicate genotypes if any are found. If 
#'   sequences are present, files are written identifying low frequency 
#'   substitutions and sequence likelihoods.\cr
#'   The return value is a list with the following elements:
#'   
#' \describe{
#'   \item{by.sample}{data.frame of by-sample summaries}
#'   \item{\code{by.locus}}{data.frame of by-locus summaries}
#'   \item{\code{dup.df}}{data.frame identifying potential duplicates}
#'   \item{\code{by.seq}}{list of low frequency substitutions and haplotype 
#'     likelihoods for each gene}
#' }
#' 
#' @author Eric Archer \email{eric.archer@@noaa.gov}
#' 
#' @seealso \code{\link{summarizeInds}}, \code{\link{summarizeLoci}}, 
#'   \code{\link{dupGenotypes}}, \code{\link{lowFreqSubs}}, 
#'   \code{\link{sequenceLikelihoods}}
#' 
#' @export
#' 
summarizeAll <- function(g, write.files = FALSE, label = NULL, ...) {
  cat("\n")
  cat(format(Sys.time()), ": Individual summaries\n")
  by.sample <- summarizeInds(g)
  
  cat(format(Sys.time()), ": Locus summaries\n")
  by.locus <- summarizeLoci(g) %>% 
    dplyr::mutate(stratum = "All") %>% 
    dplyr::select(.data$stratum, dplyr::everything()) %>% 
    dplyr::bind_rows(summarizeLoci(g, TRUE))
  
  cat(format(Sys.time()), ": Duplicate genotypes\n")
  dup.df <- dupGenotypes(g, ...)
  
  # Sequence summaries
  by.seq <- if(!is.null(getSequences(g))) {
    cat(format(Sys.time()), ": Sequence summaries\n")        
    low.freq.subs <- lowFreqSubs(g, simplify = FALSE, ...)
    seq.likelihoods <- sequenceLikelihoods(g, simplify = FALSE, ...)
    sapply(getLociNames(g), function(x) {
      list( 
        low.freq.subs = low.freq.subs[[x]],
        seq.likelihoods = seq.likelihoods[[x]]
      )
    }, simplify = FALSE)
  } else NULL
      
  if(write.files) {
    cat(format(Sys.time()), ": Writing files\n")
    # Write summaries to files
    label <- if(is.null(label)) getDescription(g) else label
    label <- gsub("[[:punct:]]", ".", label)
    fname <- paste(label, ".sample.summary.csv", sep = "")
    utils::write.csv(by.sample, file = fname, row.names = FALSE)
    fname <- paste(label, ".locus.summary.csv", sep = "")
    utils::write.csv(by.locus, file = fname, row.names = FALSE)
    
    if(!is.null(dup.df)) {
      fname <- paste(label, ".duplicate.samples.csv", sep = "")
      utils::write.csv(dup.df, file = fname, row.names = FALSE)
    }
    
    if(!is.null(by.seq)) {
      for(x in names(by.seq)) {
        fname <- paste(label, "low.freq.subs", x, "csv", sep = ".")
        utils::write.csv(by.seq[[x]]$low.freq.subs, file = fname, row.names = FALSE)
        fname <- paste(label, "sequence.likelihoods", x, "csv", sep = ".")
        utils::write.csv(by.seq[[x]]$seq.likelihoods, file = fname, row.names = FALSE)
      }
    }
  }

  cat("\n")
  invisible(
    list(
      by.sample = by.sample, 
      by.locus = by.locus, 
      dup.df = dup.df,
      by.seq = by.seq
    )
  )
}